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Dear all,
more than one negative frequency at a TS ar ea nuisance, which I had to
put up with quite a lot. I tried all the suggestions which were made
earlier, but heard with interest about the error you assigned to
frequency calculations. Could anybody recommend a paper about this?
Thanks,
Meike


From chemistry-request@server.ccl.net Wed Feb 14 07:27:45 2001
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From: "David Livingstone" <davel@chmqst.demon.co.uk>
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<color><param>0100,0100,0100</param>Hi,


<color><param>FF00,0000,0000</param>> I am looking for a review article alongwith examples on Principle

> Component Analysis as applied to QSAR. It should be written for

> beginners.

> Name: Prashant desai

> e-mail: pradesai@bol.net.in


</color>I can recommend my book (well I would, wouldn't I ?) which treats PCA and 
several related methods in QSAR:


 "Data Analysis for Chemists: Applications to QSAR and chemical product 
design" Oxford University Press, 1995, ISBN  0 19 855728 0.


I won't take up any more bandwidth here, e-mail me if you are 

interested and I can send you a table of contents and extracts from a

couple of reviews.


Dave.



<nofill>
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From chemistry-request@server.ccl.net Wed Feb 14 07:49:44 2001
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Date: Wed, 14 Feb 2001 14:49:43 +0200 (SAST)
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To all the computational Chemistry experts,

I am currently using G98 to run a few MP2 jobs with a relatively large 
basis set. However, the ".rwf" file in the scratch directory ends up
becoming so ridiculously huge and it eventually crashes the system
every time I try. Can any one please tell me how to reduce that ".rwf"
file without altering the nature of my calculations. I tried the %mem
keyword but it did not help out at all. Please please Help.

Thank you sincerely

The ignorant one
Jeff Chen





From chemistry-request@server.ccl.net Wed Feb 14 08:07:47 2001
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Try Scott and Radom, J Phys Chem, 1996, 100, 16502-16513.

The paper gives rms errors for 19 different approaches applied
to inverse frequencies for 1066 individual vibrations.

David

Meike Reinhold wrote:
> 
> Dear all,
> more than one negative frequency at a TS ar ea nuisance, which I had to
> put up with quite a lot. I tried all the suggestions which were made
> earlier, but heard with interest about the error you assigned to
> frequency calculations. Could anybody recommend a paper about this?
> Thanks,
> Meike
> 
> -= This is automatically added to each message by mailing script =-
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-- 

________________________________________________________________

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Senior Modeling Scientist              Parc Scientifique G.Besse
Computational Drug Discovery                         30000 Nimes
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From chemistry-request@server.ccl.net Wed Feb 14 10:24:00 2001
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See the article:


R. Franke and A. Gruska: "Principal Component and Factor 

Analysis", p. 113-163 in:

"Chemometric Methods in Molecular Design" /  ed. by Han van de 

Waterbeemd. - Weinheim; New York; Basel; Cambridge; Tokyo: 

VCH, 1995


On 13 Nov 00, at 11:54, Prashant Desai wrote:


<color><param>7F00,0000,0000</param>> I am looking for a review article alongwith examples on Principle

> Component Analysis as applied to QSAR. It should be written for

> beginners.

> Name: Prashant desai

> e-mail: <underline><color><param>0000,8000,0000</param>pradesai@bol.net.in

</underline><color><param>7F00,0000,0000</param>> 

> 

> -= This is automatically added to each message by mailing 
script =-

> <underline><color><param>0000,8000,0000</param>CHEMISTRY@ccl.net</underline><color><param>7F00,0000,0000</param> -- To Everybody  | <underline><color><param>0000,8000,0000</param>CHEMISTRY-
REQUEST@ccl.net</underline><color><param>7F00,0000,0000</param> -- To Admins

> <underline><color><param>0000,8000,0000</param>MAILSERV@ccl.net</underline><color><param>7F00,0000,0000</param> -- HELP CHEMISTRY or HELP SEARCH

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> Ftp: ftp.ccl.net  |  WWW: <underline><color><param>0000,8000,0000</param>http://www.ccl.net/chemistry/</underline><color><param>7F00,0000,0000</param>   | Jan: 
<underline><color><param>0000,8000,0000</param>jkl@ccl.net

</underline><color><param>7F00,0000,0000</param>> 

> 

> 

> 

> 

> 



<nofill>
--------------------------------------------------------------
Prof. R. Franke / DC A. Gruska
Consulting in Drug Design GbR    phone: +49-33397-62396
Gartenstrasse 14                 fax: +49-33397-62154
D-16352 Basdorf bei Berlin       email: drugdes@berlin.snafu.de
--------------------------------------------------------------


From chemistry-request@server.ccl.net Wed Feb 14 10:37:49 2001
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Date: Wed, 14 Feb 2001 17:37:48 +0200
From: Maija Lahtela <mlahtela@csc.fi>
To: chemistry@ccl.net
Subject: Program for planning syntheses in organic chemistry
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Dear CCLers,

I am interested in simple and easy to use (possible free and
cheap) programs that could be used in high school for teaching in organic
chemistry synthesizing planning. In the program you could give starting
compounds and program would give possible products. Or user  could give
the structure of the compund which he wishes to synthesize.

Thank in advance!

Maija Lahtela-Kakkonen

*****************************************************
Maija Lahtela-Kakkonen, 
Application Scientist / Chemistry
CSC-Scientific Computing
Tekniikantie 15 a D, P.O.Box 405 
FIN-02101 ESPOO  FINLAND
TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302
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****************************************************



From chemistry-request@server.ccl.net Wed Feb 14 11:52:18 2001
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Date: Wed, 14 Feb 2001 10:53:26 +0000
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Thanks for all replies. I have solve this problem by Ata's advice. Just
add two blank lines at the end of the molecular specification input.

Below is the question and the replies:

Hi, everyone,

Today, I tried ONIOM method to calculate a rather big system containing
a Nickel atom. I used a modified lanl2dz basis set to Ni and 6-31++G**
to all atoms in the directly coordinated groups. B3LYP was used for this

part of the molecule. PM3 was used to those substituents on the ligands.

The input file is listed below:

#P ONIOM(B3LYP/gen:PM3) Pseudo=cards opt scf=(maxcycle=256) freq

molecule specification

  Ni 0
 S    3 1.00
  0.7620000000D+01 -0.4082550000D+00
  0.2294000000D+01  0.7455308000D+00
  0.8760000000D+00  0.5325721000D+00
 S    4 1.00
  0.7620000000D+01  0.1872591000D+00
  0.2294000000D+01 -0.3966964000D+00
  0.8760000000D+00 -0.4954003000D+00
  0.1153000000D+00  0.1084434000D+01
 S    1 1.00
  0.3960000000D-01  0.1000000000D+01
 P    3 1.00
  0.2366000000D+02 -0.4815580000D-01
  0.2893000000D+01  0.6258473000D+00
  0.9435000000D+00  0.4715158000D+00
 P    4 1.00
  0.2366000000D+02  0.7131470000D-02
  0.2893000000D+01 -0.1089909500D+00
  0.9435000000D+00 -0.4615260000D-01
  0.8400000000D-01  0.8025519700D+00
 P    1 1.00
  0.2400000000D-01  0.1000000000D+01
 D    4 1.00
  0.4272000000D+02  0.3726990000D-01
  0.1176000000D+02  0.1956103000D+00
  0.3817000000D+01  0.4561273000D+00
  0.1169000000D+01  0.5621587000D+00
 D    1 1.00
  0.2836000000D+00  0.1000000000D+01
 ****
2 3 4 5 6 7 8 9 10
6-31++G**
****

 Ni 0
 lanl2dz



But, this job could not work properly and the following error message
was printed in the output file.



 Standard basis: VSTO-3G (5D, 7F)
 ===============================================================================

====================================================
 PSEUDOPOTENTIAL PARAMETERS
 ===============================================================================

====================================================
  CENTER     ATOMIC      VALENCE      ANGULAR      POWER
                               COORDINATES
  NUMBER     NUMBER     ELECTRONS     MOMENTUM     OF R
EXPONENT        COE
FFICIENT                X           Y           Z
 ===============================================================================

====================================================
  WANTED AN INTEGER AS INPUT.
  FOUND AN END-OF-LINE FOR INPUT.
 STO-3G






       ?
 Error termination via Lnk1e in /usr/local/g98.a7//g98/l301.exe.

Cannot G98 work properly when ONIOM and gen are used together? Any
advices are prefered.

Thanks in advance

Yubo

--
============================================================
Dr. Yubo Fan               Email: yubofan@mail.chem.tamu.edu
Department of Chemistry    Tel:   1-979-845-7222
Texas A&M University
College Station, TX 77843
============================================================

??????????

It's possible, look this example:

$RUNGAUSS
%chk=teste_mcg.chk
#P opt freq oniom(hf/gen:hf/gen) 6d 10f pseudo=cards

Gaussian Test:

0 1 0 1
C  0.000000    0.000000    0.000000
H  0.000000    0.000000    1.100000
O  1.125833    0.000000   -0.650000
C -1.299038    0.000000   -0.750000 L H
F -1.041506    0.000000   -2.126109 L
F -2.033682   -1.142892   -0.412219 L
F -2.033682    1.142892   -0.412219 L

@./h-0.gbs
****
@./c-0.gbs
****
@./o-0.gbs
****
@./f-0.gbs
****

C 0
C    1     2
L=1   COMPONENT
 1
     1      8.56468  -.89371
L=0   COMPONENT
 2
    0       2.81497   1.92926
    2       8.11296  14.88199
O 0
O    1     2
L=1   COMPONENT
 1
     1      16.11718   -.92550
L=0   COMPONENT
 2
    0      5.05348   1.96069
    2      15.95333 29.13442
F 0
F    1     2
L=1   COMPONENT
 1
     1     20.73959  -.93258
L=0   COMPONENT
 2
    0       6.60488    2.03649
    2       18.24092  27.86279

@./h-0.gbs
****
@./c-0.gbs
****
@./o-0.gbs
****
@./f-0.gbs
****

C 0
C    1     2
L=1   COMPONENT
 1
     1      8.56468  -.89371
L=0   COMPONENT
 2
    0       2.81497   1.92926
    2       8.11296  14.88199
O 0
O    1     2
L=1   COMPONENT
 1
     1      16.11718   -.92550
L=0   COMPONENT
 2
    0      5.05348   1.96069
    2      15.95333 29.13442
F 0
F    1     2
L=1   COMPONENT
 1
     1     20.73959  -.93258
L=0   COMPONENT
 2
    0       6.60488    2.03649
    2       18.24092  27.86279


In your case it's because PM3 tries read pseudo potentials every time
it is executed, so you must "remember" PM3 that there isn't pseudo
potentials. Leave more than 2 blank lines at the end of the input and
try again (I guess).

Ata.


--
 Ataualpa Albert Carmo Braga            atabraga@iqm.unicamp.br
                                        http://www.iqm.unicamp.br

?????????

Yubo,

In my experience, ONIOM has trouble reading pseudopotentials. Although
there might be other ways to do it (and I'd love to hear if anyone
suggests
them), you need to use an IOp to get it to work. With only one QM layer,

you might be able to just add IOP(3/17=8) to your route card. Otherwise,

you'd need to do a non-standard route, where you include the 17=8 option

in
any line that begins with 3/5=7... .

--Steve


Steven Feldgus <sfeldgus@hamilton.edu>

Subject:
         Re: CCL:Summary:DFT for hydrogen bond
     Date:
         Thu, 8 Feb 2001 17:25:44 -0200
     From:
         Ataualpa Albert Carmo Braga <atabraga@iqm.unicamp.br>
       To:
         Yubo Fan <yubofan@mail.chem.tamu.edu>
 References:
         1




>From GAMESS's manual:

MOPAC parameters exist for the following elements.
The quote means that these elements are treated as
"sparkles" rather than as atoms with genuine basis
functions.  For MNDO:

  H
 Li  *          B  C  N  O  F
 Na' *         Al Si  P  S Cl
  K' * ...  Zn  * Ge  *  * Br
 Rb' * ...   *  * Sn  *  *  I
 *   * ...  Hg  * Pb  *

          For AM1:                         For PM3:
  H                               H
  *  *          B  C  N  O  F     *  Be         *  C  N  O  F
 Na' *         Al Si  P  S Cl    Na' Mg        Al Si  P  S Cl
  K' * ...  Zn  * Ge  *  * Br     K' * ...  Zn Ga Ge As Se Br
 Rb' * ...   *  * Sn  *  *  I    Rb' * ...  Cd In Sn Sb Te  I
 *   * ...  Hg  *  *  *          *   * ...  Hg Tl Pb Bi


Ata.

--
 Ataualpa Albert Carmo Braga            atabraga@iqm.unicamp.br
                                        http://www.iqm.unicamp.br


Subject:
         Re: CCL:ONIOM and gen cannot work together
     Date:
         Thu, 8 Feb 2001 15:16:12 -0500 (EST)
    From:
         gaussian.com!csd@gaussian.com (Cust. Service Doug)
 Reply-To:
         gaussian.com!help%gaussian.com@gaussian.com
      To:
         uunet!mail.chem.tamu.edu!yubofan%gaussian.com@uunet.uu.net
(Yubo Fan)




  Dr. Fan,

   First, the ONIOM methods cannot handle this case with PM3 because
there is no PM3 parametriztion for Ni.  You do need to be careful on
using Gen and PSEUDO=CARDS as well.

   The problem with PM3 arises because the ONIOM model computes the
full model at the low level of theory and the model system at the low
level of theory, both of these require a parametrization for Ni.  You
can use UFF or a low level HF instead.

   The general basis and ECP input needs to be supplied in the order
the calculation uses it and the Pseudo=Cards forces each layer to
read an ECP input line whether it is used or not.  Rev. A.9 implements
the GenECP option to simplify this but if you choose to have GEN
on more than one level or ExtraBasis you can still encounter this.

   The order is Low level on the Real or whole system.  Next is the
medium model with the intermediate method.  Third the model system with
the high level of theory.  Then the corrections low level of theory on
the medium model, the intermediate level of theory on the model and
finally the low level of theory on the model system.  In the case where
there any two levels the three calculations using either the
intermediate
level of theory or the medium model are omitted.  The low level of
theory
on the model system is done even in the three level case where it is not

used for the ONIOM energy.

   So if you are using Rev. A.9 then switch to ONIOM(B3LYP/GenECP:UFF)
or ONIOM(B3LYP/GenECP:HF/STO-3G).  If you are using an earlier revision
you will need to include a blank line before the General basis input and

one after the general basis so that the PSEUDO=READ will get its
empty input section and proceed.
--

  Douglas J. Fox
  Technical Support
  Gaussian, Inc.
  help@gaussian.com





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From: "Shadbolt, S, Sheila" <shadbolt@psipsy.uct.ac.za>
To: pradesai@bol.net.in
Date: Wed, 14 Feb 2001 09:31:41 SAST-2
Subject: Fwd: Re: CCL:Review on Principle Component Analysis
CC: chemistry@ccl.net, Christopher.Whitehead@pfizer.com
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Here are 2 references that may help:

1) Book
Chemometrics, mathematics and statistics in chemistry.
Edited by B.R Kowalski
D. Reidel publishing company , 1984
Chapter:
Multivariate data analysis in chemistry.
pp17-95

2) Article
Principle component analysis
Wold, S., Esbensen, K. and Geladi, P.
Chemometrics and intelligent laboratory systems, 2 (1987) 37-52



Sheila Shadbolt



******************************
     
     S. Shadbolt
     Department of Chemistry
     U.C.T
     
*******************************
     


From chemistry-request@server.ccl.net Wed Feb 14 16:45:59 2001
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From: uddin@chem.wisc.edu
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Date: Wed, 14 Feb 2001 15:42:50 -0600
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Hi Jeff,

If the .rwf is the real problem, then you can split the file. You need 
to specify the location of the file on the disk where you want to 
write. The format is 

%RWF=loc1,size1,loc2,size2,...... 

You can write a line of 120 character at most. Look at chapter2 of 
gaussian98 manual for more information. The %mem is used to 
control the available dynamic memory which can't control the size 
of .rwf. 

You can also reduce the file size by suppressing some of the 
unnecessary calculations such as raman intensity in frequency 
jobs etc..

Cheers,


Jamal Uddin




On 14 Feb 01, at 14:49, Jeff Chen wrote:

> 
> 
> To all the computational Chemistry experts,
> 
> I am currently using G98 to run a few MP2 jobs with a relatively large
> basis set. However, the ".rwf" file in the scratch directory ends up
> becoming so ridiculously huge and it eventually crashes the system
> every time I try. Can any one please tell me how to reduce that ".rwf"
> file without altering the nature of my calculations. I tried the %mem
> keyword but it did not help out at all. Please please Help.
> 
> Thank you sincerely
> 
> The ignorant one
> Jeff Chen
> 
> 
> 
> 
> 
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